************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /usr/local/genome/lib/phase/PHASE2 -d1 abce1.phase.inp abce1.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST abce1.phase.out_freqs : haplotype frequency estimates abce1.phase.out_pairs : most likely haplotype pairs for each individual abce1.phase.out_recom : estimates of recombination parameters abce1.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 47 Number of Loci: 17 Positions of loci: 739 790 3581 4605 4606 5272 6281 7734 9815 16095 16644 19701 21231 22758 24827 30505 30936 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file abce1.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 AATDATGAGTAGICGGT 8.000000 2 AATDTTGAGTAGICGGT 1.000000 3 AGTDATGAGGAGICGGT 8.000000 4 AGTDATGAGTAGICGGT 5.000000 5 AGTDTTGAGTAGICGGT 4.000000 6 AGTITTGAGTAGICGGT 4.000000 7 GATDATGAGTAGICGGT 34.000000 8 GATDATGAGTAGICGAT 1.000000 9 GATDACGAGTAGICGAT 11.000000 10 GATITTGAGTAGICGGT 1.000000 11 GACDATAGGTTGDTGGC 8.000000 12 GACDATAGGTTADTCGC 4.000000 13 GACDATAGTTTGDTGGC 4.000000 14 GACDATAGTTTADTCGC 1.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY DY01: (1,3) DY02: (1,3) DY03: (7,7) DY04: (3,6) DY05: (1,5) DY06: (3,6) DY07: (1,5) DY08: (3,8) DY09: (1,7) DY10: (7,7) DY11: (1,9) DY12: (7,9) DY13: (3,7) DY14: (1,5) DY15: (3,4) DY16: (7,7) DY17: (6,7) DY18: (7,7) DY19: (6,7) DY20: (7,9) DY21: (3,7) DY22: (1,7) DY23: (2,9) DY24: (5,7) E101: (12,13) E102: (10,11) E103: (7,9) E104: (7,11) E105: (7,11) E106: (7,13) E107: (7,7) E108: (11,14) E109: (7,9) E110: (7,11) E111: (11,13) E112: (7,12) E113: (7,12) E114: (7,7) E115: (7,11) E116: (7,12) E117: (4,9) E118: (4,9) E119: (4,9) E120: (9,13) E121: (4,7) E122: (7,11) E123: (7,9) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 DY01 A A T D A T G A G T A G I C G G T A G T D A T G A G G A G I C G G T 0 DY02 A A T D A T G A G T A G I C G G T A G T D A T G A G G A G I C G G T 0 DY03 G A T D A T G A G T A G I C G G T G A T D A T G A G T A G I C G G T 0 DY04 A G T D A T G A G G A G I C G G T A G T I T T G A G T A G I C G G T 0 DY05 A (A) T D A T G A G T A G I C G G T A (G) T D T T G A G T A G I C G G T 0 DY06 A G T D A T G A G G A G I C G G T A G T I T T G A G T A G I C G G T 0 DY07 A (A) T D A T G A G T A G I C G G T A (G) T D T T G A G T A G I C G G T 0 DY08 A G T D A T G A G G A G I C G (G) T G A T D A T G A G T A G I C G (A) T 0 DY09 A A T D A T G A G T A G I C G G T G A T D A T G A G T A G I C G G T 0 DY10 G A T D A T G A G T A G I C G G T G A T D A T G A G T A G I C G G T 0 DY11 A A T D A T G A G T A G I C G G T G A T D A C G A G T A G I C G A T 0 DY12 G A T D A T G A G T A G I C G G T G A T D A C G A G T A G I C G A T 0 DY13 A G T D A T G A G G A G I C G G T G A T D A T G A G T A G I C G G T 0 DY14 A (A) T D A T G A G T A G I C G G T A (G) T D T T G A G T A G I C G G T 0 DY15 A G T D A T G A G G A G I C G G T A G T D A T G A G [T] A G I C G G T 0 DY16 G A T D A T G A G T A G I C G G T G A T D A T G A G T A G I C G G T 0 DY17 A G T I T T G A G T A G I C G G T G A T D A T G A G T A G I C G G T 0 DY18 G A T D A T G A G T A G I C G G T G A T D A T G A G T A G I C G G T 0 DY19 A G T I T T G A G T A G I C G G T G A T D A T G A G T A G I C G G T 0 DY20 G A T D A T G A G T A G I C G G T G A T D A C G A G T A G I C G A T 0 DY21 A G T D A T G A G G A G I C G G T G A T D A T G A G T A G I C G G T 0 DY22 A A T D A T G A G T A G I C G G T G A T D A T G A G T A G I C G G T 0 DY23 A A T D (T) T G A G T A G I C G G T G A T D (A) C G A G T A G I C G A T 0 DY24 A G T D (T) T G A G T A G I C G G T G A T D (A) T G A G T A G I C G G T 0 E101 G A C D A T A G (G) T T A D T C G C G A C D A T A G (T) T T G D T G G C 0 E102 G A T (I) T T G A G T A G I C G G T G A C (D) A T A G G T T G D T G G C 0 E103 G A T D A T G A G T A G I C G G T G A T D A C G A G T A G I C G A T 0 E104 G A T D A T G A G T A G I C G G T G A C D A T A G G T T G D T G G C 0 E105 G A T D A T G A G T A G I C G G T G A C D A T A G G T T G D T G G C 0 E106 G A T D A T G A G T A G I C G G T G A C D A T A G T T T G D T G G C 0 E107 G A T D A T G A G T A G I C G G T G A T D A T G A G T A G I C G G T 0 E108 G A C D A T A G G T T G D T G G C G A C D A T A G T T T [A] D T C G C 0 E109 G A T D A T G A G T A G I C G G T G A T D A C G A G T A G I C G A T 0 E110 G A T D A T G A G T A G I C G G T G A C D A T A G G T T G D T G G C 0 E111 G A C D A T A G G T T G D T G G C G A C D A T A G T T T G D T G G C 0 E112 G A T D A T G A G T A G I C G G T G A C D A T A G G T T A D T C G C 0 E113 G A T D A T G A G T A G I C G G T G A C D A T A G G T T A D T C G C 0 E114 G A T D A T G A G T A G I C G G T G A T D A T G A G T A G I C G G T 0 E115 G A T D A T G A G T A G I C G G T G A C D A T A G G T T G D T G G C 0 E116 G A T D A T G A G T A G I C G G T G A C D A T A G G T T A D T C G C 0 E117 A G T D A T G A G T A G I C G G T G A T D A C G A G T A G I C G A T 0 E118 A G T D A T G A G T A G I C G G T G A T D A C G A G T A G I C G A T 0 E119 A G T D A T G A G T A G I C G G T G A T D A C G A G T A G I C G A T 0 E120 G A T D A C G A G T A G I C G A T G A C D A T A G T T T G D T G G C 0 E121 A G T D A T G A G T A G I C G G T G A T D A T G A G T A G I C G G T 0 E122 G A T D A T G A G T A G I C G G T G A C D A T A G G T T G D T G G C 0 E123 G A T D A T G A G T A G I C G G T G A T D A C G A G T A G I C G A T END BESTPAIRS1 Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in [] with phase known positions indicated by = BEGIN BESTPAIRS2 0 DY01 = A = = = = = ? ? T ? ? = = = = = = G = = = = = ? ? G ? ? = = = = = 0 DY02 = A = = = = = = = T = = = = = = = = G = = = = = = = G = = = = = = = 0 DY03 = = ? = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = 0 DY04 = = = D A = = = = G = = = = = = = = = = I T = = = = T = = = = = = = 0 DY05 = (A) = = A = = = = = = = = = = = = = (G) = = T = = = = = = = = = = = = 0 DY06 = = = D A = = = ? G = ? = = = = = = = = I T = = = ? T = ? = = = = = 0 DY07 = (A) = = A = = ? = = ? ? = = = = = = (G) = = T = = ? = = ? ? = = = = = 0 DY08 A G = = = = = = = G = = = = = (G) ? G A = = = = = = = T = = = = = (A) ? 0 DY09 A = = = = = = = = = = = = = = ? ? G = = = = = = = = = = = = = = ? ? 0 DY10 = = = = = = = = = = ? = = = = = = = = = = = = = = = = ? = = = = = = 0 DY11 A = = = = T = = = = = = = = = G = G = = = = C = = = = = = = = = A = 0 DY12 = = = = = T = = = = = ? = = = ? ? = = = = = C = = = = = ? = = = ? ? 0 DY13 A G = = = = = = = G = = = = = = = G A = = = = = = = T = = = = = = = 0 DY14 = (A) = = A = = = = = = = = = = = = = (G) = = T = = = = = = = = = = = = 0 DY15 = = = = = = = = = ? = = = = = = = = = = = = = = = = ? = = = = = = = 0 DY16 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 DY17 A G = I T = = = = = = = = = = ? ? G A = D A = = = = = = = = = = ? ? 0 DY18 = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = ? = 0 DY19 A G = I T = = = = = = = = = = = = G A = D A = = = = = = = = = = = = 0 DY20 = = = = = T = = = = = = = = = G = = = = = = C = = = = = = = = = A = 0 DY21 A G = = = = = = = G = = = = = = = G A = = = = = = = T = = = = = = = 0 DY22 A = = = = = = = = = ? = = ? = = = G = = = = = = = = = ? = = ? = = = 0 DY23 A = = = (T) T = = = = = ? = ? = G = G = = = (A) C = = = = = ? = ? = A = 0 DY24 A G = = (T) = = = = = = = = = = = = G A = = (A) = = = = = = = = = = = = 0 E101 = = = = = = = = (G) ? = A = = C = = = = = = = = = = (T) ? = G = = G = = 0 E102 = = T (I) T = G A = = A = I C = = T = = C (D) A = A G = = T = D T = = C 0 E103 = = = = = T = = = = = = = = = G = = = = = = C = = = = = = = = = A = 0 E104 = = T = = = G A = = A = I C = = T = = C = = = A G = = T = D T = = C 0 E105 = = T = = = G A = = A ? ? C = = T = = C = = = A G = = T ? ? T = = C 0 E106 = = T = = = G A G = A = I C = = T = = C = = = A G T = T = D T = = C 0 E107 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E108 = = = = = = = = G = = ? = ? G = = = = = = = = = = T = = ? = ? C = = 0 E109 = = = = = T = = = = = = = = = ? ? = = = = = C = = = = = = = = = ? ? 0 E110 = = T = = = G A = = A = I C = = T = = C = = = A G = = T = D T = = C 0 E111 = = = = = = = = G = = = = = = = = = = = = = = = = T = = = = = = = = 0 E112 = = T = = = G A = = A G I C G = T = = C = = = A G = = T A D T C = C 0 E113 = = T = = = G A = = A G I C G ? T = = C = = = A G = = T A D T C ? C 0 E114 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E115 = = T = = = G A = = A = I C = = T = = C = = = A G = = T = D T = = C 0 E116 = = T = = = G A = = A G I C G = T = = C = = = A G = = T A D T C = C 0 E117 A G = = = T = = = = = = ? = = G = G A = = = C = = = = = = ? = = A = 0 E118 A G = = = T = = = = = = = = = G = G A = = = C = = = = = = = = = A = 0 E119 A G = = = T = = = = = = = = = G = G A = = = C = = = = = = = = = A = 0 E120 = = T = = C G A G = A = ? C = A T = = C = = T A G T = T = ? T = G C 0 E121 A G = = = = = ? = = = ? = ? = = = G A = = = = = ? = = = ? = ? = = = 0 E122 = = T = = = G A = = A = I ? = = T = = C = = = A G = = T = D ? = = C 0 E123 = = = = = T = = = = = = = = = G = = = = = = C = = = = = = = = = A = END BESTPAIRS2 Phase probabilities at each site with phase known positions indicated by = and missing data positions indicated by ? BEGIN PHASEPROBS = 0.97 = = = = = ? ? 1.00 ? ? = = = = = = 0.98 = = = = = = = 1.00 = = = = = = = = = ? = = = = = = = = = = = = = = = = = 1.00 1.00 = = = = 1.00 = = = = = = = = 0.52 = = 1.00 = = = = = = = = = = = = = = = 1.00 1.00 = = = ? 1.00 = ? = = = = = = 0.51 = = 1.00 = = ? = = ? ? = = = = = 1.00 1.00 = = = = = = = 1.00 = = = = = 0.62 ? 1.00 = = = = = = = = = = = = = = ? ? = = = = = = = = = = ? = = = = = = 0.98 = = = = 1.00 = = = = = = = = = 1.00 = = = = = = 1.00 = = = = = ? = = = ? ? 1.00 1.00 = = = = = = = 1.00 = = = = = = = = 0.51 = = 1.00 = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = 0.93 0.93 = 1.00 1.00 = = = = = = = = = = ? ? = = = = = = = = = = = = = = = ? = 0.93 0.93 = 1.00 1.00 = = = = = = = = = = = = = = = = = 1.00 = = = = = = = = = 1.00 = 1.00 1.00 = = = = = = = 1.00 = = = = = = = 1.00 = = = = = = = = = ? = = ? = = = 1.00 = = = 0.84 1.00 = = = = = ? = ? = 1.00 = 1.00 0.94 = = 0.87 = = = = = = = = = = = = = = = = = = = = 0.73 ? = 1.00 = = 1.00 = = = = 1.00 0.90 0.95 = 1.00 1.00 = = 1.00 = 1.00 1.00 = = 1.00 = = = = = 1.00 = = = = = = = = = 1.00 = = = 1.00 = = = 1.00 1.00 = = 1.00 = 1.00 1.00 = = 1.00 = = 1.00 = = = 1.00 1.00 = = 1.00 ? ? 1.00 = = 1.00 = = 1.00 = = = 1.00 1.00 1.00 = 1.00 = 1.00 1.00 = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = ? = ? 1.00 = = = = = = = 1.00 = = = = = = = = = ? ? = = 1.00 = = = 1.00 1.00 = = 1.00 = 1.00 1.00 = = 1.00 = = = = = = = = 1.00 = = = = = = = = = = 1.00 = = = 1.00 1.00 = = 1.00 1.00 1.00 1.00 1.00 = 1.00 = = 1.00 = = = 1.00 1.00 = = 1.00 1.00 1.00 1.00 1.00 ? 1.00 = = = = = = = = = = = = = = = = = = = 1.00 = = = 1.00 1.00 = = 1.00 = 1.00 1.00 = = 1.00 = = 1.00 = = = 1.00 1.00 = = 1.00 1.00 1.00 1.00 1.00 = 1.00 0.92 0.92 = = = 1.00 = = = = = = ? = = 1.00 = 0.92 0.92 = = = 1.00 = = = = = = = = = 1.00 = 0.93 0.93 = = = 1.00 = = = = = = = = = 1.00 = = = 1.00 = = 1.00 1.00 1.00 1.00 = 1.00 = ? 1.00 = 1.00 1.00 0.99 1.00 = = = = = ? = = = ? = ? = = = = = 1.00 = = = 1.00 1.00 = = 1.00 = 1.00 ? = = 1.00 = = = = = 1.00 = = = = = = = = = 1.00 = END PHASEPROBS